checkColumns
(Package: miRNApath) :
Check data.frame for Required Columns
Internal function designed to assist checking for required columns in a data.frame.
● Data Source:
BioConductor
● Keywords: internal, manip
● Alias: checkColumns
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convertFoldChange
(Package: miRNApath) :
Converts Fold Change to Consistent Format
The script tries to determine if the fold changes are in an expected format, and if not, does its best to convert correctly. Internal function.
● Data Source:
BioConductor
● Keywords: internal, manip
● Alias: convertFoldChange
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This method filters the miRNApath data to denote hits versus non-hits, the required distinction for running the enrichment algorithm. Data is expected to have been loaded by the loadmirnapath method.
● Data Source:
BioConductor
● Keywords: manip
● Alias: filtermirnapath
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This method loads data from a tab-delimited flatfile into an object of type mirnapath to be used for further miRNA analysis.
● Data Source:
BioConductor
● Keywords: IO, manip
● Alias: loadmirnapath
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loadmirnapathways
(Package: miRNApath) :
Load gene to pathway associations for miRNApath
This method loads associations between genes and the pathways to which they belong.
● Data Source:
BioConductor
● Keywords: IO, attribute, manip
● Alias: loadmirnapathways
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loadmirnatogene
(Package: miRNApath) :
Load miRNA to gene associations for miRNApath
This method loads associations between miRNAs to the genes they affect.
● Data Source:
BioConductor
● Keywords: IO, attribute, manip
● Alias: loadmirnatogene
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This package provides methods for assessing the statistical over-representation of miRNA effects on gene sets, using supplied miRNA-to-gene associations. Because these associations are notably many-to-many (one miRNA to many genes; one gene affected by many miRNAs) the assessment is complex and warrants perhaps different approaches than are classically performed on differential gene expression datasets.
● Data Source:
BioConductor
● Keywords: htest, package
● Alias: miRNApath-package
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mirnaTable
(Package: miRNApath) :
Create miRNA Enrichment Summary Table as data.frame
This function takes an miRNApath object which has been evaluated by runEnrichment(), and provides a data.frame summary.
● Data Source:
BioConductor
● Keywords: manip
● Alias: mirnaTable
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mirnapath-class
(Package: miRNApath) :
S4 class mirnapath and its "show" method
miRNApath class intended to contain miRNA data, gene and pathway associations, and ultimately the pathway enrichment results in detail.
● Data Source:
BioConductor
● Keywords: classes
● Alias: mirnapath-class, show,mirnapath-method
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runEnrichment
(Package: miRNApath) :
Perform gene set enrichment analysis on a miRNApath
This method performs a hypergeometric enrichment analysis on a miRNApath object, which should already contain miRNA data, miRNA-gene associations, gene-pathway associations, and some criteria for filtering miRNA hits from the full tested set.
● Data Source:
BioConductor
● Keywords: htest
● Alias: runEnrichment
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